Identification of the key genes implicated in the transformation of OLP to OSCC using RNA-sequencing

Comparative Analysis of Transposable Elements Reveals the Diversity of Transposable Elements in Decapoda and Their Effects on Genomic Evolution

Transposable elements (TEs) are mobile genetic elements that exist in the host genome and exert considerable influence on the evolution of the host genome. Since crustaceans, including decapoda, are considered ideal models for studying the relationship between adaptive evolution and TEs, TEs were identified and classified in the genomes of eight decapoda species and one diplostraca species (as the outgroup) using two strategies, namely homology-based annotation and de novo annotation. The statistics and classification of TEs showed that their proportion in the genome and their taxonomic composition in decapoda were different. Moreover, correlation analysis and transcriptome data demonstrated that there were more PIF-Harbinger TEs in the genomes of Eriocheir sinensis and Scylla paramamosain, and the expression patterns of PIF-Harbingers were significantly altered under air exposure stress conditions. These results signaled that PIF-Harbingers expanded in the genome of E. sinensis and S. paramamosain and might be related to their air exposure tolerance levels. Meanwhile, sequence alignment revealed that some Jockey-like sequences (JLSs) with high similarity to specific regions of the White spot syndrome virus (WSSV) genome existed in all eight decapod species. At the same time, phylogenetic comparison exposed that the phylogenetic tree constructed by JLSs was not in agreement with that of the species tree, and the distribution of each branch was significantly different. The abovementioned results signaled that these WSSV-specific JLSs might transfer horizontally and contribute to the emergence of WSSV. This study accumulated data for expanding research on TEs in decapod species and also provided new insights and future direction for the breeding of stress-resistant and disease-resistant crab breeds.

Identification of key genes and small molecule drugs in osteoarthritis by integrated bioinformatics analysis

Background

Osteoarthritis (OA) is a common joint degenerative disease that can affect multiple joints. Genetic events may play an important regulatory role in the early stages of the disease, but the specific mechanisms have not yet been fully elucidated. The main purpose of this study was to screen for disease-causing hub genes and effective small molecule drugs to reveal the pathogenesis of OA and to develop novel drugs for treatment.

Methods

Two gene expression profile datasets, GSE55235 and GSE55457, were integrated and further analyzed. The consistently differentially expressed genes (DEGs) were identified, and functional annotation and pathway analysis of these genes were performed with GO and KEGG. A protein-protein interaction network (PPI) of the DEGs was generated using STRING, and potential small molecule drug screening was performed on the connectivity map (CMap).

Results

A total of 158 consistently differentially expressed genes were identified from the two profile datasets. The functions of these DEGs are mainly related to the TNF signaling pathway, osteoclast differentiation, MAPK signaling pathway and so on. The PPI network contains 127 nodes and 1802 edges, and the ten hub genes were interleukin 6 (IL6), vascular endothelial growth factor A (VEGFA)and so on. 7 small molecule drugs were identified as potential interactors with these hubs.

Conclusions

This study explains the disorder of expression in the pathological process of OA at transcriptome, which will help to understand the pathogenesis of OA.

Differential transcriptome analysis of Sporocytophaga sp. CX11 and identification of candidate genes involved in lignocellulose degradation

Cellulose is the most abundant renewable bioresources on earth, and the biodegradation and utilization of cellulose would contribute to the sustainable development of global environment. Sporocytophaga species are common aerobic cellulose-degrading bacteria in soil, which can adhere to the surface of cellulose matrix and motile by gliding. In this study, a differential transcriptome analysis of Sporocytophaga sp. CX11 was performed and a total of 4,217 differentially expressed genes (DEGs) were identified. Gene Ontology enrichment results showed that there are three GO categories related to cellulose degradation function among the annotated DEGs. A total of 177 DEGs were identified as genes encoding carbohydrate-active enzymes (CAZymes), among which 54 significantly upregulated CAZymes were mainly cellulases, hemicellulases, pectinases, etc. 39 DEGs were screened to associate with gliding function. In order to explore unannotated genes potentially related to cellulose metabolism, cluster analysis was performed using the Short-Time Series Expression Miner algorithm (STEM). 281 unannotated genes were predicted to be associated with the initial-middle stage of cellulose degradation and 289 unannotated genes might function in the middle-last stage of cellulose degradation. Sporocytophaga sp. CX11 could produce extracellular endo-xylanase, endo-glucanase, FPase and β-glucosidase, respectively, according to different carbon source conditions. Altogether, this study provides valuable insights into the transcriptome information of Sporocytophaga sp. CX11, which would be useful to explore its application in biodegradation and utilization of cellulose resources.

Oral Lichen Planus and Oral Squamous Cell Carcinoma share key oncogenic signatures

To investigate similarities in the gene profile of Oral Lichen Planus and Oral Squamous Cell Carcinoma that may justify a carcinogenic potential, we analyzed the gene expression signatures of Oral Lichen Planus and Oral Squamous Cell Carcinoma in early and advanced stages. Based on gene expression data from public databases, we used a bioinformatics approach to compare expression profiles, estimate immune infiltrate composition, identify differentially and co-expressed genes, and propose putative therapeutic targets and associated drugs. Our results revealed gene expression patterns related to processes of keratinization, keratinocyte differentiation, cell proliferation and immune response in common between Oral Lichen Planus and early and advanced Oral Squamous Cell Carcinoma, with the cornified envelope formation and antigen processing cross-presentation pathways in common between Oral Lichen Planus and early Oral Squamous Cell Carcinoma. Together, these results reveal that key tumor suppressors and oncogenes such as PI3, SPRR1B and KRT17, as well as genes associated with different immune processes such as CXCL13, HIF1A and IL1B are dysregulated in OLP.

Massive expansion of P-selectin genes in two Venerida species, Sinonovacula constricta and Mercenaria mercenaria: evidence from comparative genomics of Bivalvia

Background

P-selectin is a molecule participating in the inflammatory response through mediating cellular adhesion and essential for wound repair. However, studies regarding P-selectin in Bivalvia are rare. This study identified 90 P-selectin genes among nine bivalve genomes and classified them into 4 subfamilies according to phylogenetic analysis.

Results

Notable P-selectin gene expansion was observed in two Venerida species, Sinonovacula constricta and Mercenaria mercenaria. The synteny analysis revealed that P-selectin gene expansion was mostly caused by tandem duplication. In addition, the expression profiles of P-selectin genes in S. constricta showed that many P-selectins were specifically highly expressed in the gills, and the P-selectin expression patterns changed dramatically under low salt stress and ammonia nitrogen stress.

Conclusions

The massive expansion of P-selectins may facilitate the tolerance to environmental stresses. This study sheds light on the characterizations and expression profiles of P-selectin genes in Bivalvia and provides an integrated framework for further investigation of the role of P-selectins in the environmental tolerance of bivalves.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08861-6.

The genomic and proteomic landscape in oral lichen planus versus oral squamous cell carcinoma: a scoping review

BACKGROUND

Oral lichen planus (OLP), a World Health Organization (WHO)-classified oral potentially malignant condition, confers a 1% risk of transformation to oral squamous cell carcinoma (OSCC). There does not appear to be a consensus understanding of the underlying molecular events. This scoping review aimed to identify critical molecular pathways and highlight gaps in existing knowledge on malignant transformation in OLP.

METHODS

Following Preferred Reporting Items for Systematic Reviews and Meta-Analysis Protocols (PRISMA-P) guidelines, a comprehensive literature search and methodical screening identified 61 relevant studies detailing molecular differences between OLP and OSCC.

RESULTS

Molecular changes shared between OLP and OSCC included those affecting cellular proliferation (altered p53 expression, hypermethylation of p16/CDKN2A, MYC gains, increased ki-67), apoptosis (increased bcl-2 and survivin expression), extracellular matrix (ECM) remodeling (increased matrix metalloproteinase [MMP] expression), and transcriptional control (altered bmi1 and microRNA [miRNA] expression). In addition, some molecular alterations accumulated incrementally from control to OLP to OSCC or were present in higher-risk erosive variants of OLP or transformed OLP. Few studies included rigorous diagnostic inclusion criteria or unbiased discovery methods.

CONCLUSIONS

Results of this review support the potentially malignant nature of OLP and imply that molecular events associated with malignant transformation may be heterogeneous. In addition, findings in this review highlight the need for additional studies using rigorous diagnostic inclusion criteria and unbiased discovery methods to further understand this process.

Comprehensive Analysis of Tumor Immune Microenvironment Characteristics for the Prognostic Prediction and Immunotherapy of Oral Squamous Cell Carcinoma

Background: Oral squamous cell carcinoma (OSCC) is the most common cancer of oral and maxillofacial region. A recent clinical research has shown that tumor immune microenvironment (TIME)cells are closely related to immunotherapy sensitivity and OSCC prognosis. Nonetheless, a comprehensive analysis of TIME in OSCC has not been reported.

Methods: Bioinformatics and computational algorithms were employed to determine the significance of TIME cells in 257 OSCC patients. TIME scores were measured by three TIME models, and then used to evaluate the prognosis of OSCC patients.

Results: High TIME score was characterized by better prognosis in OSCC patients less than 60 years old, overexpression of immunotherapy targets (e.g., PD-1 and CLTA-4), and higher T-cell activity to inhibit tumor growth. Besides, poor prognosis was associated with low time score.

Conclusion: TIME score exhibited potential as a prognostic biomarker and an indicator in predict immunotherapeutic outcomes. Through the understanding of TIME model, this study can provide a better scheme for immunotherapy as the effective treatment of OSCC patients in the future.

Identification and Expression Analyses of Invertase Genes in Moso Bamboo Reveal Their Potential Drought Stress Functions

Invertases (INVs) can irreversibly hydrolyze sucrose into fructose and glucose, which play principal roles in carbon metabolism and responses to various stresses in plants. However, little is known about the INV family in bamboos, especially their potential function in drought stress. In this study, 29 PeINVs were identified in moso bamboo (Phyllostachys edulis). They were clustered into alkaline/neutral invertase (NINV) and acid invertase (AINV) groups based on the gene structures, conserved motifs, and phylogenetic analysis results. The collinearity analysis showed nine segmental duplication pairs within PeINVs, and 25 pairs were detected between PeINVs and OsINVs. PeINVs may have undergone strong purification selection during evolution, and a variety of stress and phytohormone-related regulatory elements were found in the promoters of PeINVs. The tissue-specific expression analysis showed that PeINVs were differentially expressed in various moso bamboo tissues, which suggested that they showed functional diversity. Both the RNA-seq and quantitative real-time PCR results indicated that four PeINVs were significantly upregulated under drought stress. Co-expression network and Pearson’s correlation coefficient analyses showed that these PeINVs co-expressed positively with sugar and water transport genes (SWTGs), and the changes were consistent with sugar content. Overall, we speculate that the identified PeINVs are spatiotemporally expressed, which enables them to participate in moso bamboo growth and development. Furthermore, PeINVs, together with SWTGs, also seem to play vital roles in the response to drought stress. These results provide a comprehensive information resource for PeINVs, which will facilitate further study of the molecular mechanism underlying PeINVs involvement in the response to drought stress in moso bamboo.

Gene signatures associated with barrier dysfunction and infection in oral lichen planus identified by analysis of transcriptomic data

Oral lichen planus (OLP) is one of the most prevalent oral mucosal diseases, but there is no cure for OLP yet. The aim of this study was to gain insights into the role of barrier dysfunction and infection in OLP pathogenesis through analysis of transcriptome datasets available in public databases. Two transcriptome datasets were downloaded from the Gene Expression Omnibus database and analyzed as whole and as partial sets after removing outliers. Differentially expressed genes (DEGs) upregulated in the dataset of OLP versus healthy epithelium were significantly enriched in epidermal development, keratinocyte differentiation, keratinization, responses to bacterial infection, and innate immune response. In contrast, the upregulated DEGs in the dataset of the mucosa predominantly reflected chemotaxis of immune cells and inflammatory/immune responses. Forty-three DEGs overlapping in the two datasets were identified after removing outliers from each dataset. The overlapping DEGs included genes associated with hyperkeratosis (upregulated LCE3E and TMEM45A), wound healing (upregulated KRT17, IL36G, TNC, and TGFBI), barrier defects (downregulated FRAS1 and BCL11A), and response to infection (upregulated IL36G, ADAP2, DFNA5, RFTN1, LITAF, and TMEM173). Immunohistochemical examination of IL-36γ, a protein encoded by one of the DEGs IL36G, in control (n = 7) and OLP (n = 25) tissues confirmed the increased expression of IL-36γ in OLP. Collectively, we identified gene signatures associated with hyperkeratosis, wound healing, barrier defects, and response to infection in OLP. IL-36γ, a cytokine involved in both wound repair and antimicrobial defense, may be a possible therapeutic target in OLP.

Tumor-educated leukocytes mRNA as a diagnostic biomarker for non-small cell lung cancer

Background

This study aimed to investigate the diagnostic and prognostic role of tumor‐educated leukocytes (TELs) mRNA in Chinese patients with non‐small cell lung cancer (NSCLC).

Methods

The TELs collected underwent total RNA isolation. RNA‐sequencing (RNA‐seq) technology was used to analyze the transcriptome of the TELs. The mRNA expression levels of differential genes were analyzed by RT‐qPCR. Statistical analyses were performed using Prism and SPSS by Mann–Whitney nonparametric test, Kruskal‐Wallis test and one‐way ANOVA.

Results

We used RNA‐seq technology to screen 95 differential genes (DEGs) from seven NSCLC and four controls, wherein 15 genes were upregulated, and 80 were downregulated. Of these, four genes were selected for further analysis, wherein one was upregulated (GPX1) and three were downregulated (BCL9L, MAP3K7CL, PCSK7). RT‐qPCR was performed in 431 samples (237 NSCLC, 194 healthy donors). The four‐gene panel showed significant differences (p < 0.001) in the expression levels between NSCLC and healthy samples. ROC curves of the panel revealed an AUC of 0.803, with a sensitivity of 73.8% and specificity of 75.3%. GPX1, BCL9L and PCSK7 genes distinguished early‐stage NSCLC patients from healthy group (p < 0.05). When the three genes were combined to diagnose early‐stage NSCLC, the diagnostic efficacy was 0.772, sensitivity was 73.7%, and specificity was 72.2%. In addition, the downregulated gene BCL9L was associated with chemotherapeutic effect.

Conclusions

The present study provided a systematic description of gene expression profiling in the TELs. It is worth noting that these four genes may be potential candidate genes for NSCLC diagnostic biomarkers and provide a basis for further biological and functional studies.

The circ-AMOTL1/ENO1 Axis Implicated in the Tumorigenesis of OLP-Associated Oral Squamous Cell Carcinoma

BACKGROUND

Oral squamous cell carcinoma (OSCC) may develop from a variety of oral potentially malignant disorders, but the mechanism of malignant transformation is still unknown. Among them, oral lichen planus (OLP) has a high prevalence. Previous studies have shown that α-enolase (ENO1) can promote cell proliferation and play an important role in tumorigenesis. In this study, we aim to explore the mechanism of ENO1 regulation in the process of OSCC tumorigenesis from OLP.

METHODS

ENO1 expression in tissues was determined by real-time quantitative PCR and immunohistochemistry. ENO1 was knocked down in cal-27 to observe the change in cell proliferation. Then, RNA-seq and bioinformatics analyses were conducted between OLP and OSCC samples. The expression of circ-AMOTL1, miRNA-22-3p, and miRNA-1294 was assessed using the real-time quantitative PCR. With knockdown and overexpression of circ-AMOTL1 in vitro, the change of ENO1 in the mRNA level was also assessed.

RESULTS

ENO1 was enhanced in the OSCC samples in comparison with OLP. Immunohistochemistry and real-time quantitative PCR results showed that ENO1 was significantly higher in OSCC tissue than in the OLP group, with a statistically significant difference (p<0.05). When ENO1 was knocked down in cal-27, cell proliferation was inhibited (p<0.05). The expression of miR-22-3p and miR-1294 was decreased in OSCC tissues, whereas ENO1 and circ-AMOTL1 increased. In an in vitro study, knockdown of circ-AMOTL1 resulted in a decrease of ENO1, while overexpression of circ-AMOTL1 led to an increase of ENO1 in the mRNA level.

CONCLUSION

We confirmed that ENO1 expression was elevated in OSCC and increased cell proliferation. In an in vitro study, ENO1 expression was promoted by circ-AMOTL1. ENO1 may play a role as a tumor-promoting gene in OSCC through the circ-AMOTL1/miR-22-3p/miR-1294 network. These novel findings may shed further light on the pathogenesis from OLP to OSCC and the potential precursor markers.

Development and verification of a personalized immune prognostic feature in breast cancer

IMPACT STATEMENT

Breast cancer is among the highest prevalent malignant tumors worldwide with a low survival ratio. Immune-related genes have great potential as prognostic indicator in many types of tumors. Therefore, we have attempted to develop immune-related gene markers to enhance the prognosis of breast cancer. 17-IRGPs signature was constructed as a newly developed prognostic indicator to predict the survival of BC patients.

Metabolic changes during malignant transformation in primary cells of oral lichen planus: Succinate accumulation and tumour suppression

Oral squamous cell carcinoma (OSCC) is usually diagnosed at late stages, which leads to high morbidity. There are evidence that chronic inflammation (eg oral lichen planus [OLP]) was a risk factor of OSCC, but often misdiagnosed or ignored until invasion and metastasis. By applying precision medicine, the molecular microenvironment variations and relevant biomarkers for the malignant transformation from OLP to OSCC can be fully investigated. Several studies pointed out that the metabolic pathway were suppressed in OSCC. However, it remains unclear how the systemic profile of the metabolites change during the malignant transformation. In this study, we examined and compared the mucosa samples from 11 healthy individuals, 10 OLP patients and 21 OSCC patients. Based on the results, succinate, a key metabolite of the tricarboxylic acid cycle pathway, was accumulated in the primary cultured precancerous OLP keratinocytes and OSCC cells. Then, we found that succinate activated the hypoxia‐inducible factor‐1 alpha (HIF‐1α) pathway and induced apoptosis, which could also be up‐regulated by the tumour suppressor lncRNA MEG3. These results suggested the critical roles of succinate and MEG3 in the metabolic changes during malignant transformation from OLP to OSCC, which indicated that succinate, HIF1α and downstream proteins might serve as new biomarkers of precancerous OLP for early diagnosis and therapeutic monitoring. In addition, succinate or its prodrugs might become a potential therapy for the prevention or treatment of OSCC.

Weighted gene co-expression network analysis and prognostic analysis identifies hub genes and the molecular mechanism related to head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is a lethal disease with suboptimal survival outcomes. In this study, we aimed to find an independent prognostic factor of head and neck squamous cell carcinoma and investigate its effect on tumor cell proliferation, apoptosis, migration progress and cell cycle phase. Weighted gene co-expression network analysis (WGCNA) is an analysis method for mining module information in chip data through soft threshold. In this article, it was used to divide differential genes into different modules and determined the ten hub genes. Overall survival (OS) and disease-free survival (DFS) analyses as well as univariate and multivariate regression analyses were used to figure out HMGA2 as the independent prognostic factor. RT-qPCR and western blot results revealed the HMGA2 expression levels. Via colony formation, flow cytometry and wound healing assays, we tested the involvement of HMGA2 knockdown in corresponding cancer cell biological behaviors. HMGA2 level was up-regulated in HNSCC tissues and cell lines (SCC-25 and FaDu) in comparison with their normal counterparts. HMGA2 knockdown decreased cancer cell proliferation, promoted cell apoptosis, blocked cell cycle at G0/G1 phase, and inhibited cell migration. We regarded HMGA2 as a potential diagnostic and therapeutic target of HNSCC.

A genome-wide association scan of biological processes involved in oral lichen planus and oral squamous cell carcinoma

BACKGROUND

In this study, the molecular mechanisms underlying malignant transformation from oral lichen planus (OLP) to oral squamous cell carcinoma (OSCC) were examined.

METHODS

High-throughput sequencing of long noncoding RNAs (lncRNAs) and mRNAs of normal subjects and patients with OLP and OSCC was conducted. RNA-seq reads were mapped, lncRNA and mRNA transcripts were assembled, and expression levels were estimated. The targets of lncRNAs were predicted. Finally, Gene Ontology (GO) and pathway enrichment analyses of differentially expressed genes (DEGs) and lncRNA targets were performed.

RESULTS

High-quality sequence data were generated and the mapping ratios for OSCC, normal, and OLP samples were high. In total, 820, 656, and 582 DEGs were obtained from OPL vs. normal, OSCC vs. normal, and OSCC vs. OPL, respectively. A total of 1721 known lncRNAs and 133 predicted lncRNAs and targets were obtained. Keratinization was significantly enriched by OSCC-related DEGs, but not OPL-related DEGs. The pathway of olfactory transduction was enriched by OPL- and OSCC-related DEGs. Defense response to virus and viral carcinogenesis were enriched by DEGs and lncRNA targets in all comparisons. GO term related to the metabolic process was enriched by lncRNA targets in the OPL vs normal comparison, and antigen processing and presentation via MHC class I was significantly enriched by lncRNA targets in the other 2 comparisons.

CONCLUSION

Keratinization and MHC class I antigen processing and presentation were activated during the malignant transformation from OLP to OSCC. Additionally, the olfactory transduction pathway may be important for OSCC.